{
  "_id": "6ae7573c2e87f76f20accfe2",
  "Package": "SPsimSeq",
  "Title": "Semi-parametric simulation tool for bulk and single-cell RNA\nsequencing data",
  "Version": "1.23.0",
  "Authors@R": "c(person(given = \"Alemu Takele\",\nfamily = \"Assefa\",\nrole = c(\"aut\"),\nemail = \"alemutak@hotmail.com\"),\nperson(given = \"Olivier\",\nfamily = \"Thas\",\nrole = c(\"ths\"),\nemail = \"Olivier.Thas@ugent.be\"),\nperson(given = \"Joris\",\nfamily = \"Meys\",\nrole = c(\"cre\"),\nemail = \"Joris.Meys@ugent.be\"),\nperson(given = \"Stijn\",\nfamily = \"Hawinkel\",\nrole = c(\"aut\"),\nemail = \"stijnhawinkel@hotmail.com\"))",
  "Description": "SPsimSeq uses a specially designed exponential family for\ndensity estimation to constructs the distribution of gene\nexpression levels from a given real RNA sequencing data\n(single-cell or bulk), and subsequently simulates a new dataset\nfrom the estimated marginal distributions using\nGaussian-copulas to retain the dependence between genes. It\nallows simulation of multiple groups and batches with any\nrequired sample size and library size.",
  "License": "GPL-2",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "URL": "https://github.com/CenterForStatistics-UGent/SPsimSeq",
  "biocViews": "GeneExpression, RNASeq, SingleCell, Sequencing, DNASeq",
  "RoxygenNote": "7.1.0",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libuv1-dev\nlibxml2-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:52:57 UTC",
  "RemoteUrl": "https://github.com/bioc/SPsimSeq",
  "RemoteRef": "HEAD",
  "RemoteSha": "72d88fe83edbdf2bcbcc993a08bdec977ca35ca3",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-11-01 13:22:13 UTC",
    "User": "root"
  },
  "Author": "Alemu Takele Assefa [aut],\nOlivier Thas [ths],\nJoris Meys [cre],\nStijn Hawinkel [aut]",
  "Maintainer": "Joris Meys <Joris.Meys@ugent.be>",
  "_user": "bioc",
  "_type": "src",
  "_file": "SPsimSeq_1.23.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/3accdf1444b6014e089bc8fe7e4e01256a39375a0bece5923fcd81a9d32b5e49",
  "_filesize": 1126012,
  "_sha256": "3accdf1444b6014e089bc8fe7e4e01256a39375a0bece5923fcd81a9d32b5e49",
  "_expires": "2027-02-09T15:14:02.000Z",
  "_created": "2026-11-01T13:22:13.000Z",
  "_published": "2026-11-01T15:14:04.194Z",
  "_upstream": "https://github.com/bioc/SPsimSeq",
  "_status": "success",
  "_maintainer": {
    "name": "Joris Meys",
    "email": "joris.meys@ugent.be",
    "login": "jofam",
    "mastodon": "@JorisMeys@mstdn.social",
    "description": "",
    "uuid": 809906
  },
  "_jobs": [
    {
      "job": 124861126006,
      "time": 190,
      "config": "bioc-checks",
      "r": "4.6.2",
      "check": "WARNING",
      "artifact": "13085764557"
    },
    {
      "job": 124861125934,
      "time": 387,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "13086517710"
    },
    {
      "job": 124861125992,
      "time": 453,
      "config": "linux-release-x86_64",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13085663676"
    },
    {
      "job": 124861125964,
      "time": 282,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "13088628524"
    },
    {
      "job": 124861125935,
      "time": 316,
      "config": "macos-release-arm64",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13088687188"
    },
    {
      "job": 124857706186,
      "time": 394,
      "config": "source",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13085287802"
    },
    {
      "job": 124861125930,
      "time": 131,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "13086397757"
    },
    {
      "job": 124861126076,
      "time": 350,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "13085860796"
    },
    {
      "job": 124861126020,
      "time": 302,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "13086120996"
    },
    {
      "job": 124861126015,
      "time": 317,
      "config": "windows-release-x86_64",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13085364136"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 11
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/41309242452",
  "_commit": {
    "id": "72d88fe83edbdf2bcbcc993a08bdec977ca35ca3",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777380777
  },
  "_distro": "resolute",
  "_host": "GitHub-Actions",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0",
      "role": "Depends"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "SingleCellExperiment",
      "role": "Imports"
    },
    {
      "package": "fitdistrplus",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "edgeR",
      "role": "Imports"
    },
    {
      "package": "Hmisc",
      "role": "Imports"
    },
    {
      "package": "WGCNA",
      "role": "Imports"
    },
    {
      "package": "limma",
      "role": "Imports"
    },
    {
      "package": "mvtnorm",
      "role": "Imports"
    },
    {
      "package": "phyloseq",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "LSD",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.23.0",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.22.0",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "geneexpression",
    "rnaseq",
    "singlecell",
    "sequencing",
    "dnaseq"
  ],
  "_stars": 10,
  "_contributors": [
    {
      "user": "sthawinke",
      "count": 108,
      "uuid": 22496974
    },
    {
      "user": "alemuta",
      "count": 28,
      "uuid": 28293463
    },
    {
      "user": "alemutakele",
      "count": 4,
      "uuid": 21121112
    },
    {
      "user": "jofam",
      "count": 1,
      "uuid": 809906
    },
    {
      "user": "katrinleinweber",
      "count": 1,
      "uuid": 9948149
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 482,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 479,
    "source": "https://www.bioconductor.org/packages/stats/bioc/SPsimSeq"
  },
  "_mentions": 4,
  "_devurl": "https://github.com/centerforstatistics-ugent/spsimseq",
  "_searchresults": 33,
  "_abi": {
    "exports": [
      {
        "key": "SPsimSeq::generic:extractMat",
        "hash": "d27d986253827864"
      }
    ],
    "imports": []
  },
  "_rbuild": "4.6.2",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/SPsimSeq.html"
  ],
  "_homeurl": "https://github.com/centerforstatistics-ugent/spsimseq",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "configExperiment",
    "evaluateDensities",
    "SPsimSeq"
  ],
  "_datasets": [
    {
      "name": "scNGP.data",
      "title": "Neuroblastoma NGP cells single-cell RNA-seq.",
      "object": "scNGP.data",
      "class": [
        "SingleCellExperiment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "zhang.data.sub",
      "title": "Neuroblastoma bulk RNA-seq data retrieved from Zhang et (2015).",
      "object": "zhang.data.sub",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "SPsimSeq-package",
      "title": "SPsimSeq package",
      "topics": [
        "SPsimSeq-package"
      ]
    },
    {
      "page": "buildXmat",
      "title": "An auxialiary function to quickly construct the polyomial matrix, using Horner's rule",
      "topics": [
        "buildXmat"
      ]
    },
    {
      "page": "calculateCPM",
      "title": "Calculates counts per millions of reads, possibly with log-transform",
      "topics": [
        "calculateCPM"
      ]
    },
    {
      "page": "checkInputValidity",
      "title": "Check for data validity",
      "topics": [
        "checkInputValidity"
      ]
    },
    {
      "page": "chooseCandGenes",
      "title": "Select candidate genes",
      "topics": [
        "chooseCandGenes"
      ]
    },
    {
      "page": "configExperiment",
      "title": "Configure experiment",
      "topics": [
        "configExperiment"
      ]
    },
    {
      "page": "constructDens",
      "title": "Construct the cumulative density",
      "topics": [
        "constructDens"
      ]
    },
    {
      "page": "estLibSizeDistr",
      "title": "Estimate log-normal distribution for the library sizes",
      "topics": [
        "estLibSizeDistr"
      ]
    },
    {
      "page": "evaluateDensities",
      "title": "Evaluate the densities in the estimated SPsimSeq object",
      "topics": [
        "evaluateDensities"
      ]
    },
    {
      "page": "expit",
      "title": "Evaluate the expit function",
      "topics": [
        "expit"
      ]
    },
    {
      "page": "extractMat",
      "title": "A function with S4 dispatching to extract the count matrix",
      "topics": [
        "extractMat",
        "extractMat,data.frame-method",
        "extractMat,matrix-method",
        "extractMat,phyloseq-method",
        "extractMat,SingleCellExperiment-method"
      ]
    },
    {
      "page": "fitLLmodel",
      "title": "Fit log linear model for each gene",
      "topics": [
        "fitLLmodel"
      ]
    },
    {
      "page": "fitPoisGlm",
      "title": "Fast fit Poisson regression",
      "topics": [
        "fitPoisGlm"
      ]
    },
    {
      "page": "fracZeroLogitModel",
      "title": "Extract data and iterate over batches to estimate zero probability models",
      "topics": [
        "fracZeroLogitModel"
      ]
    },
    {
      "page": "genCopula",
      "title": "Generate a copula instance",
      "topics": [
        "genCopula"
      ]
    },
    {
      "page": "geneParmEst",
      "title": "Gene level param estimates for density estimation",
      "topics": [
        "geneParmEst"
      ]
    },
    {
      "page": "genLibSizes",
      "title": "Generate library sizes from log-normal",
      "topics": [
        "genLibSizes"
      ]
    },
    {
      "page": "matchCopula",
      "title": "Match copulas to estimated SP distribution",
      "topics": [
        "matchCopula"
      ]
    },
    {
      "page": "obtCorMatsBatch",
      "title": "A function to obtain copulas or uniform random variables",
      "topics": [
        "obtCorMatsBatch"
      ]
    },
    {
      "page": "obtCount",
      "title": "Calculates height and mid points of a distribution",
      "topics": [
        "obtCount"
      ]
    },
    {
      "page": "parmEstDensVec",
      "title": "Density estimation on a single vector",
      "topics": [
        "parmEstDensVec"
      ]
    },
    {
      "page": "prepareSPsimOutputs",
      "title": "A function to prepare outputs",
      "topics": [
        "prepareSPsimOutputs"
      ]
    },
    {
      "page": "samZeroID",
      "title": "Return ID for observations to be set to zero",
      "topics": [
        "samZeroID"
      ]
    },
    {
      "page": "scNGP.data",
      "title": "Neuroblastoma NGP cells single-cell RNA-seq.",
      "topics": [
        "scNGP.data"
      ]
    },
    {
      "page": "selectGenes",
      "title": "Sample genes from candidate genes",
      "topics": [
        "selectGenes"
      ]
    },
    {
      "page": "SPsimPerGene",
      "title": "A function that generates the simulated data for a single gene",
      "topics": [
        "SPsimPerGene"
      ]
    },
    {
      "page": "SPsimSeq",
      "title": "A function to simulate bulk or single cell RNA sequencing data",
      "topics": [
        "SPsimSeq"
      ]
    },
    {
      "page": "zeroProbModel",
      "title": "Predict zero probability using logistic rgression",
      "topics": [
        "zeroProbModel"
      ]
    },
    {
      "page": "zhang.data.sub",
      "title": "Neuroblastoma bulk RNA-seq data retrieved from Zhang et (2015).",
      "topics": [
        "zhang.data.sub"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/SPsimSeq/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "ade4",
    "ape",
    "backports",
    "base64enc",
    "Biobase",
    "BiocGenerics",
    "biomformat",
    "Biostrings",
    "bslib",
    "cachem",
    "checkmate",
    "cli",
    "cluster",
    "codetools",
    "colorspace",
    "cpp11",
    "crayon",
    "data.table",
    "DelayedArray",
    "digest",
    "doParallel",
    "dynamicTreeCut",
    "edgeR",
    "evaluate",
    "farver",
    "fastcluster",
    "fastmap",
    "fitdistrplus",
    "fontawesome",
    "foreach",
    "foreign",
    "Formula",
    "fs",
    "generics",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "gridExtra",
    "gtable",
    "highr",
    "Hmisc",
    "htmlTable",
    "htmltools",
    "htmlwidgets",
    "igraph",
    "impute",
    "IRanges",
    "isoband",
    "iterators",
    "jquerylib",
    "jsonlite",
    "knitr",
    "labeling",
    "lattice",
    "lifecycle",
    "limma",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mgcv",
    "mime",
    "multtest",
    "mvtnorm",
    "nlme",
    "nnet",
    "permute",
    "phyloseq",
    "pixmap",
    "pkgconfig",
    "plyr",
    "preprocessCore",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "reshape2",
    "rlang",
    "rmarkdown",
    "rpart",
    "rstudioapi",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "Seqinfo",
    "SingleCellExperiment",
    "sp",
    "SparseArray",
    "statmod",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "survival",
    "tinytex",
    "vctrs",
    "vegan",
    "viridisLite",
    "WGCNA",
    "withr",
    "xfun",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "SPsimSeq.Rmd",
      "filename": "SPsimSeq.html",
      "title": "Manual for the SPsimSeq package: semi-parametric simulation for bulk and single cell RNA-seq data",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Contents",
        "Introduction to SPsimSeq",
        "Installing SPsimSeq",
        "Demonstration",
        "Example 1: simulating bulk RNA-seq",
        "Example 2: simulating single-cell RNA-seq (containing read-counts)",
        "References"
      ],
      "created": "2020-04-01 18:56:12",
      "modified": "2020-05-15 13:45:20",
      "commits": 6
    }
  ],
  "_score": 7.199755177253475,
  "_indexed": true,
  "_nocasepkg": "spsimseq",
  "_universes": [
    "bioc",
    "jofam",
    "centerforstatistics-ugent"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.23.0",
      "date": "2026-11-01T13:55:01.000Z",
      "distro": "resolute",
      "commit": "72d88fe83edbdf2bcbcc993a08bdec977ca35ca3",
      "fileid": "https://r2.ropensci.org/4f7587f72347e9e1dc424c12b2344aa74a0992f964dca20f3335ed26d9c4f180",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309242452"
    },
    {
      "r": "4.6.2",
      "os": "linux",
      "version": "1.23.0",
      "date": "2026-11-01T13:54:56.000Z",
      "distro": "resolute",
      "commit": "72d88fe83edbdf2bcbcc993a08bdec977ca35ca3",
      "fileid": "https://r2.ropensci.org/8cefe625574da5db28f3fde50870a68b197a3170486a8c992fec567c4727a643",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309242452"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.23.0",
      "date": "2026-11-01T15:10:06.000Z",
      "commit": "72d88fe83edbdf2bcbcc993a08bdec977ca35ca3",
      "fileid": "https://r2.ropensci.org/094e7a24c80439e38c29e9bcd0d705029bb2d555b44585da9a4470cbab5e22f9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309242452"
    },
    {
      "r": "4.6.2",
      "os": "mac",
      "version": "1.23.0",
      "date": "2026-11-01T15:09:52.000Z",
      "commit": "72d88fe83edbdf2bcbcc993a08bdec977ca35ca3",
      "fileid": "https://r2.ropensci.org/5c6e3a5f26660af81cbf298d8aa9a8653ea5c20e0ccc86a99c0dee1bf3b198fb",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309242452"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.23.0",
      "date": "2026-11-01T13:53:42.000Z",
      "commit": "72d88fe83edbdf2bcbcc993a08bdec977ca35ca3",
      "fileid": "https://r2.ropensci.org/92fed0d78a580adf4a214e648d1a4209460e1c02fd80d07ce550d01c4a20f7f0",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309242452"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.23.0",
      "date": "2026-11-01T13:31:56.000Z",
      "commit": "72d88fe83edbdf2bcbcc993a08bdec977ca35ca3",
      "fileid": "https://r2.ropensci.org/5d390cac578110a5f228dddffbef5d968f52e5c4b17aef4dcd9a7383b5321017",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309242452"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.23.0",
      "date": "2026-11-01T13:32:01.000Z",
      "commit": "72d88fe83edbdf2bcbcc993a08bdec977ca35ca3",
      "fileid": "https://r2.ropensci.org/c04e3898be0bdc8641dc90792f16e73fad571f48b550cca8da584ad0938796c5",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309242452"
    },
    {
      "r": "4.6.2",
      "os": "win",
      "version": "1.23.0",
      "date": "2026-11-01T13:32:02.000Z",
      "commit": "72d88fe83edbdf2bcbcc993a08bdec977ca35ca3",
      "fileid": "https://r2.ropensci.org/b15d5dcfe3599e19520a5938e5cfcb28f7476a6f76fb8d8b38beaf4840a913c5",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309242452"
    }
  ]
}